update enclone/enclone_paper/src/scoper/autopilot_master.sh and instructions

[ssnn-airr]

Hi! I am trying to run the scoper code used in the enclone paper, with a new version of the immcantation container, that fixes the parallelization issue you refer to in enclone/enclone_paper/src/scoper/autopilot.R.

Should build_immcantation_inputs in enclone/enclone_paper/src/scoper/autopilot_master.sh be build_clonotyping_inputs?

I am new to rust and I am figuring things out. It would be helpful if you could provide a little more detail on how to reproduce the analysis, in particular adding instructions on paths from where to run things, and when/how to use cargo, rustc...